Dear Ram; you can check fao website. There are lots of information about your question in FAO website.

http://www.fao.org/docrep/t8598e/t8598e05.htm#4.3 fish pond culture

ftp://ftp.fao.org/fi/cdrom/fao_training/FAO_Training/General/x6706e/x6706e12.htm

I also recommend you to read the information in FAO sites, as mentioned  by Mustafa. 

GIS based multicriteria analysis method can be adopted

I'll echo Habib and some of the others above.  Certainly seasonal availability of water, soil composition and drainage types, endemic species.  Don't forget seasonal flooding histories, and also past land usage, that is avoiding sites that may be industrially contaminated or impacted by adjacent agricultural usage (herbicide, pesticide applications on adjacent lands).

The better location of aquaculture farms depends on, cultured species, method (intensive, semi-intensive, hiper-intensive, recirculation, biofloc), the feed used (protein content), the adjacent environment (land based, coastal zone, river, etc.). The methods implemented to minimize the environmental impacts, as water reuse (aquaponia) or agriculture; waste reuse (solids as fertilizers, or biogas production).

If you have different options is recommendable to develop the matrix of environmental impact (EIM) to each one. This is an example:

Assessment Larry W. Canter: ftp://www.energia.bme.hu/pub/hullgazd/Environmental%20Engineers'%20Handbook/Ch02.pdf